Sequencing-by-synthesis is among a new generation of high throughput DNA sequencing technologies. Examples of techniques and platforms for sequencing-by-synthesis include the Genome Analyzer/HiSeq/MiSeq platforms (Illumina, Inc.; see, e.g., U.S. Pat. Nos. 6,833,246 and 5,750,341); those applying pyrosequencing-based sequencing methods such as that used by Roche/454 Technologies on the GS FLX, GS FLX Titanium, and GS Junior platforms (see, e.g., Ronaghi et al., SCIENCE, 281:363 (1998) and Margulies et al., NATURE, 437:376-380 (2005)); and those by Life Technologies Corp./Ion Torrent in the PGM™ system (see, e.g., U.S. Patent Application Publication Nos. 2010/0137143 and 2009/0026082, which are incorporated by reference in their entirety). As will be further explained below, one of the problems in sequencing-by-synthesis is the loss of phase synchrony and/or signal droop, which can hinder the ability to make accurate base calls. More accurate estimates of the phasing effects and/or signal droop can improve the ability to make accurate base calls.